Introduction

• What questions are best answered using tags?
• What questions are you using tags to answer?

• Study species: Ziphius cavirostris
• Tag: DTAG3

Controlled Exposure Experiments (CEEs)

with Mid-frequency Active Sonar (MFAS)

• Can the question be answered with existing data?
• Are simulations a viable alternative?
• Is the tag suitable?
  • sensors, sampling rates
  • accuracy
  • size
  • tagging duration

• Lack of existing data for analysis or simulation
• Was tag suitable?
  • What sound did whales receive?
  • Do dive behavior, body movement or foraging behavior indicate response?

• Do you need and have a permit?
  • NOAA permits to approach, photograph and tag in SOCAL
• Do you have IACUC and peer approval?
  • IACUC proposals and many public presentations, consults

• How will you minimize risk to animals and personnel?
  • Field protocols, sound source shut-down, data recovery
    
    (photo from https://www.national-park.com/welcome-to-channel-islands-national-park/)

• How many animals will you need to tag to answer the question? (TWO?)
• How will you measure responses to tagging (during or after field work)?
• Can you collect and integrate all of the ancillary data needed?

• Visual observations
• Acoustic tracking
• Visual and radar tracking of vessels in the area
• Photos and video
• Genetics (biopsy, skin sample)
• Life history of tagged whale (photo-id studies)
• Oceanographic measurements (CTD, current, bathymetry)

• Storage, quality control, archiving (paper? the dreaded spreadsheets?)
• Accounting for effort
• Collaboration with others in the study area, data sharing
• Integrating data with different time scales, varying accuracy

• How will you analyse the data to address your question?
• Who else can use the data?
• When and how will you share the data?
• Does the value of the science merit the abuse?
  
  (photo from Dietz et al. 2007, doi.org/10.1186/1472-6785-7-14)

• Short-term (day) to Long-term (year)
• Attachment: suction cups, bolts, straps, glue…
• Sensors: Geo position, orientation, depth/altitude, sound, video, heart-rate, temperature…
• Archival vs. Telemetry

• Availability of tags & analysis tools
• “Ease” of attachment (for you and animal)
• Record duration vs. data density
• “Ease” of data retrieval

• What question are you trying to answer?
• Is your tag appropriate?
• You (may have chosen)…

• Typically include:
  • Sensors sampled multiple times per second
  • Accelerometers to measure body posture and sudden movements or changes in speed
  • Magnetometers to measure direction of travel
  • Pressure sensors to measure dive depth in aquatic or marine animals

• May include:
  • Speed sensor
  • Gyroscopes (to measure turning rate)
  • Sound sensors
  • Video recorders

• Matlab
  • Pros: Broad user base, flexible, fast at matrix calculations
  • Cons: Expensive, steep learning curve
• Octave
  • Pros: Free & open source, “almost matlab” now
  • Cons: Basic user interface, steep learning curve
• R/RStudio
  • Pros: Free & open source, pro stats standard, tutorials/resources
  • Cons: Slower (?), steep learning curve

Check out some online learning resources gathered at:

https://github.com/stacyderuiter/TagTools/wiki/Software

Learn and contribute at

http://www.animaltags.org

It's a wiki - join us!

• Tag tools can read in:
  • Raw data from several tag types
  • archival format netCDF files (<– our focus)
• NetCDF files (.nc) must be stored locally before reading.
• Assume we have a file stored at C:\data\testset1.nc
• R:
  

testset1 <- load_nc('C:\data\testset1.nc')

• Matlab/Octave:

testset1 = load_nc('C:\data\testset1.nc') ;

Still working on this - will be a VERY brief description of what/why, e.g. raw to scientific units, tag to whale frame. Details left for next lecture.

Metadata has at least 2 sources:

• Gleaned automatically from tag data files
• User-provided

Still working on this one - will include metadata gleaning example (I hope) plus screen shots of Ye Joo's metadata entry tool.

netCDF format…

• Developed with NSF funds for geoscience community
• Is flexible, accomodates data and metadata fields
• Allows many user-defined fields
• Supported by well-defined standards and conventions
• “supports a view of data as a collection of self-describing, portable objects that can be accessed through a simple interface” (-NetCDF website)

Animal Telemetry Network (ATN) Data Assembly Center (DAC)

Animal Telemetry Network (ATN) Data Assembly Center (DAC)

• In R, all “tools” must be bundled in packages.
• To use a package, you must:
  • Install the package (one-time-only)
  • Load the package (every new R session)

Option A) Install “development version” from GitHub

#install.packages('devtools')
devtools::install_github(
  'stacyderuiter/TagTools/R/tagtools')

Option B) Install from your memory stick. In RStudio:

• Select the Packages tab in the lower right pane
• Click Install
• Choose Install from package archive file
• Click Browse and navigate to the R tagtools zip file on your memory stick
• Click Install!

• Matlab has access to all functions that are:
  • In directories that are on the Matlab Path
  • In the user's current directory (“Current Folder” in GUI)

• Unpack the Matlab tagtools zip file on your computer
• In Matlab, in the Home tab, click Set Path
• Click Add with Subfolders and then select the tagtools directory
• Click Save to save the modified path

• Octave has access to all functions that are:
  • In the user's current directory (“File Browser” in GUI)
  • In packages that have been
    • installed (one-time operation) and
    • loaded (every new Octave session)

To install the tag tools package (assuming the Matlab/Octave zip file is stored in F:\tagtools\matlab), run:

pkg install tagtools0.0.0.tar.gz

Then to load it:

pkg load tagtools

In Octave, you also need to manually install and load the packages:

• netcdf
• signal

If you are online, you can simply run (for example):

pkg install netcdf 
pkg load netcdf

For specific tools, help is only a command away. Example: need help with the function plott()?

in Matlab/Octave:

help plott

in R:

?plott

No documentation for 'plott' in specified packages and libraries:
you could try '??plott'

• As possible, save data, code, and documents in subdirectories of one main project directory
• Document your work:
  • Save files rather than just running code in the console
  • Document your code with comments and explantions
  • Give variables names that are easy to understand
  • Prefer descriptive labels to numeric identifiers
• Consider Reproducible Research - code, documentation and report all in one document!
  • In R: knitr
  • In R: Rmarkdown
  • In Octave/Matlab… ?

(Stay tuned…Maybe after a coffee.)

What is wrong (or right) with this picture? [coming soon]

• Show screen shots of projects
• metadata file creation by “Homer”
• tags on animals (ethics, tag type, benefits…)
• errors you will see in R/matlab/octave